We have proteomics data from three different strains of T7 after 1, 5, and 9 minutes of infection in E. coli. Each time point has 2 replicates for a total of 18 samples.

evol: evolved phage with codon-modified gene 10

atten: initial codon-modified gene 10 phage

wt: wild-type phage

Normalization: Data are normalized by total protein area (T7 and E. coli) for each sample after computing areas or adjusting spectral counts with APEX.

Motivation for using APEX

Analyses by John Houser indicate that APEX-normalized spectral counts in E. coli corrlate more strongly with transcript levels than peak areas correlate with transcripts. These analyses examine APEX-normalized spectral counts for phage proteins.

Areas for major capsid protein show least variation

Major capsid protein: spectral counts

Major capsid protein: APEX-normalized spectral counts

Major capsid protein: areas

Do we expect APEX to perform well with very highly expressed genes?

Major capsid protein levels are suppressed in attenuated and evolved strains

APEX-normalized spectral counts

Peak areas

Some phage proteins immediately downstream of gp10A are also suppressed

Apex-normalized spectral counts

Peak areas

In aggregate, phage protein levels (not including major capsid) look about the same across strains

Class 3 protein levels (not including capsid) look roughly the same

Averaged across all genes and all replicates for a given time point and given strain, class 3 protein levels look similar to gp10A (just barely). I have not actually tested to see if any strain is significantly different from another across all genes.

Classes 1 and 2 also look roughly the same across all three strains

Some class 3 genes behave like gp10A, some do not

Above is a detailed breakdown of every class 3 gene. Several genes follow the same pattern as gp10A, but others do not.